The cloning of nucleic acid fragments as molecular libraries has become a core method used in many research, forensic and clinical settings. Current methods for molecular library construction require the ligation of double-stranded adapters of defined nucleotide sequence to the template nucleic acid ends followed by polymerase chain reaction (PCR) amplification (Bently, D. R et al. Nature, 2008, 456:53-59; Ranade, S. S. et al. Analyt. Biochem., 2009, 390:126-135). Due, in part, to the poor efficiency of the adapter ligation reaction, these methods require large quantities of starting template nucleic acid which, in some instances, may be difficult to obtain. Moreover, existing methods are prone to producing adapter-dimers, which are inhibitory side products that necessitate the purification of the intended nucleic acid products by gel electrophoresis and extraction. Such purification requirements render existing amplification methods incompatible with high-throughput multiplexed robotic methods, thereby limiting the number of different libraries that can be created at one time.